The medical and technological progress of contemporary societies has led to a notable increase in the average life expectancy of humanity. As a result, the aging population is experiencing constant and rapid growth. Consequently, there is a significant increase in the incidence of chronic diseases. This phenomenon is largely due to the decisive role that chronological age plays as a predisposing factor for conditions such as diabetes (Longo et al., 2019), cardiovascular diseases (North and Sinclair, 2012), respiratory diseases (Cho and Stout-Delgado, 2020), cancer (Berben et al., 2021), and musculoskeletal problems (Briggs et al., 2016).

Aging is a universal and progressive process of deterioration of physiological functions and the accumulation of damage in cells and tissues, ultimately leading to death (Guo et al., 2022). Although the processes that trigger and drive aging are not yet fully understood, a series of 12 hallmarks that drive and accelerate this process have been proposed. These include genomic instability, telomere shortening, epigenetic alterations, loss of proteostasis, deactivation of autophagy, deregulation in nutrient sensing, mitochondrial dysfunction, cellular senescence, loss of stem cells, alterations in intercellular communication, chronic inflammation, and imbalance of microbial homeostasis (dysbiosis) (López-Otín et al., 2023).

The biological and molecular processes that drive life are complex and highly regulated phenomena, controlled primarily by the functional organization of genes rather than their expression levels. It has been suggested that gene organization and expression are structured in modular networks (Mark et al., 2019). However, it is known that this functional organization and modularity tend to diminish or be lost with age (Southworth et al., 2009a), which could lead to malfunctioning cellular processes. The causes of this loss of functional coordination due to aging are currently unknown. Nonetheless, it has been proposed that aging has a stochastic component, related to the accumulation of regulatory errors in transcription, translation, and metabolism pathways due to the inefficiency of signaling cascades in the network and responses to environmental factors (Podolskiy et al., 2015; Lea et al., 2019). Other unknown aspects of the loss and decline in functional organization include the life stage at which it begins and the influence of sex.

Functional organization within the cell or an organism is not solely determined by gene expression levels but is rather the result of a delicate process of co-regulation between genes, transcription factors, and non-coding species (Sinha et al., 2020; Yap and Greenberg, 2018). This co-expression regulation process more accurately reflects the overall state of a cell over time (Glass et al., 2013). Frequently, approaches from physics and computational sciences have been employed to explore the co-expression patterns within a phenotype. A prime example of such an approach is co-expression networks (Mähler et al., 2017; Hernández-Lemus et al., 2019). This tool can help observe globally how pairs of genes maintain dependent relationships within a given phenotype (Ovens et al., 2021; García-Cortés et al., 2020). These relationships, collectively, can reflect the state of a phenotype and, at the same time, serve to compare different phenotypes, either between conditions or the same condition at different points in time (Espinal-Enríquez et al., 2017; Nakamura-García and Espinal-Enríquez, 2023).

In this study, through the analysis of gene co-expression networks, we explore the changes that occur in the transcriptome structure across three life stages: youth, midlife, and aging. Additionally, we analyze the differences in the functional organization of the transcriptome between men and women, using skeletal muscle as our study model, which is a postmitotic tissue. Postmitotic cells are an excellent system for studying the effects of aging, as they originate from mitotic stem cells that irreversibly lose their ability to proliferate upon differentiation. These cells can persist and function for extended periods within the organism, accumulating significant damage and aberrations that impact their function. These cells cannot be stimulated to proliferate by any physiological stimulus, nor by non-physiological stimuli such as oncogene expression or radiation. Unlike mitotic cells, postmitotic cells never undergo tumorigenic transformation (Campisi and Warner., 2001).

The loss of muscle mass and functionality associated with aging, known as sarcopenia, is a public health issue as it weakens and disables patients. Diagnosing this complex condition is challenging since there is no official guide for its diagnosis or progression. Sarcopenia exhibits significant sexual dimorphism, with a higher prevalence in men (19.2%) than in women (8.6%) (Du et al., 2019). The reasons for this difference are not yet fully understood, but hormonal changes have been suggested as important factors (Messier et al., 2011).

In this study, we have identified some changes in the functional organization patterns of skeletal muscle genes that exhibit sexual dimorphism and could contribute to the onset and progression of sarcopenia. For instance, women of all ages, unlike men, maintain the functional organization of genes involved in processes such as macroautophagy, sarcomere organization, vesicle coating, protein ubiquitination, and vesicle targeting, which might be essential for muscle maintenance. Moreover, women show a greater number of unique biological processes, suggesting greater flexibility in functional organization. This might mean that the age-related loss of biological processes does not affect women as much, as they possess alternative or complementary processes to the lost ones. Additionally, the unique transcriptional program of each sex/age deteriorates less in women than in men, as elderly women maintain the size of their transcriptional program during aging compared to men.

The biological and molecular mechanisms of sarcopenia are not well understood. However, several have been proposed, including the imbalance between muscle protein synthesis (MPS) and degradation (MPB) (Kim et al., 2020), anabolic resistance (Haran et al., 2012), chronic inflammation (Dalle et al., 2017), poor absorption and metabolism of nutrients, especially amino acids (Cholewa et al., 2017), loss and remodeling of motor units (Kung et al., 2014), ribosomal biogenesis malfunction (Melouane et al., 2019), and mitochondrial dynamics alterations (Melouane et al., 2019). Specifically, we found significant changes in the latter two biological processes, as shown in Figure 7. Our results suggest that changes in co-expression patterns might be responsible for the decline or malfunction of processes associated with mitochondrial dynamics, including mitochondrial gene expression control, mitochondrial membrane organization, electron transport, and ATP production. Interestingly, there is no loss of co-expression of these genes, but significant rewiring of their networks. This rewiring could be a major cause of the decline in mitochondrial functionality associated with aging. Similarly, the functional organization of genes controlling ribosome biogenesis and assembly changes or is lost with age, potentially impacting muscle protein synthesis.

Regarding the common genes in the giant component, as shown in Figure 4 and Supplementary Material S3, two key observations emerge: the number of shared genes is substantial in both cases, and for young phenotypes, there are several unique genes present in the giant component. This finding aligns with the previously mentioned results, which indicate a greater number of biological functions in young phenotypes, particularly concerning reproductive functions in young females. Additionally, the high number of unique genes in young males may suggest an important reservoir of genes that could be activated under certain conditions, with this reservoir diminishing as aging progresses.

The presence of common processes, despite unique gene interactions in each network, exemplifies how processes carrying out essential functions for the organism might adapt to each age’s conditions. Metabolic processes, translation, or ribosomal RNA processing involve more genes in young groups, both men and women, but also in middle-aged and old women. This may be because, during youth, women require a greater number of genes for specific functions, likely related to reproductive, metabolic and hormonal needs. This result of more robust GCNs in females has been previously reported, finding that within the gene modules of female networks there is a greater number of genes compared to males (Sutherland et al., 2019) in addition to occurring in the GCNs of practically all tissues, with these differences in wiring being mainly driven by estrogen (Chen et al., 2016). It has been proposed that these differences could be due to hormonal factors or the effect of sex chromosomes (Van Nas et al., 2009).

Young and elderly groups are expected to differ more in gene expression and biological processes. As illustrated in Figures 3, 4, 7, the number of shared processes between young and elderly phenotypes is lower compared to other age group comparisons. This is largely because networks representing older phenotypes show fewer enriched processes. We hypothesize that this reduction is linked to the loss of genetic plasticity observed with aging, which aligns with both our findings and the current understanding of the aging process. Young individuals usually have more active regenerative capacities, while the elderly might experience more cellular damage accumulation and aging-related changes (Muñoz-Cánoves et al., 2020). This is observed in men, as there are no shared biological processes between young and old men, except for positive regulation of RNA metabolic process. However, this prediction does not hold for women, as certain biological processes related to vesicle formation and transport (like COPII vesicle coating, vesicle coating, and vesicle targeting, rough ER to cis-Golgi) are shared between young and old women. These are essential processes for muscle maintenance and function, as well as oxidative stress regulation.

Contrary to expectations, there are few similarities in biological processes between sexes of the same age. Nevertheless, young men and women share some processes, mainly related to protein generation and processing (mRNA splicing, via spliceosome, positive regulation of transcription initiation from RNA polymerase II promoter, transcription by RNA polymerase I, maturation of 5.8S rRNA, protein-containing complex assembly ERAD pathway, positive regulation of cellular amide metabolic process, actomyosin structure organization). These processes are related to muscle growth and repair, as young individuals tend to have greater tissue regeneration capacity (Muñoz-Cánoves et al., 2020).

Various studies have reported the loss of gene correlation as a common characteristic of aging (Southworth et al., 2009b; Bernard et al., 2022; Levy et al., 2020). However, our results suggest that the loss of co-expression could begin during middle age, and the changes observed in aging would be a consequence of alterations at earlier ages. Additionally, our results suggest that during aging, gene coordination could be slightly recovered.

The observation that the degradation of gene co-expression networks is more pronounced during middle age, followed by a slight recovery in aging, may be related to several biological and adaptive factors, such as stress response strategies. During middle age, the body experiences significant changes in terms of metabolism, cellular function, and accumulation of molecular damage. This could cause a more abrupt dysregulation in gene coordination. However, in old age, compensatory mechanisms could be activated, such as the activation of cellular stress response pathways (autophagy, chaperones, etc.), which attempt to restore a certain level of homeostasis. This could explain a slight recovery of co-expression in old age. On the other hand, as people age, the most damaged or dysfunctional cells could be eliminated, while those that survive tend to be more resistant. In older people, co-expression networks may be more aligned with cells adapted for survival under chronic stress conditions, which could reflect a partial recovery. Additionally, the middle-age stage may be marked by a transition where cells re-evaluate the balance between growth, repair, and maintenance. As the body ages, there may be a shift towards prioritizing maintenance and survival functions rather than growth, which could lead to a partial stabilization of co-expression networks.

Notably, elderly men do not share any biological processes with elderly women. Elderly men have processes related to enzymatic activity regulation, macromolecule synthesis, and glucose metabolism, suggesting that metabolic processes might be less efficient in elderly men due to changes in co-expression. On the other hand, elderly women exhibit processes related to stress response, post-translational protein modifications, and membrane protein regulation.

It has been proposed that the functioning of a living organism heavily depends on the functional coordination of its genes and that the loss of this coordination leads to the onset and progression of pathological states (Ge et al., 2022). Additionally, it is known that aging leads to a loss of functional organization and gene modularity (Southworth et al., 2009a). However, our results suggest that the loss of functional organization and modularity might begin in middle age (40–59 years), indicating that this loss could be a primary cause of aging-associated deterioration. Thus, we propose the loss of co-expression as a potential new universal marker of aging. This presents an opportunity for developing therapeutic interventions aimed at maintaining or preventing the loss of functional gene coordination, potentially resulting in healthy aging.

In this study, through a co-expression network analysis, we have been able to identify sets of common and unique processes across three age ranges: youth, maturity, and old age. We also observed these differences by sex. In summary, the main findings of this work can be enumerated as follows.

• Networks of any age and sex present a giant component, suggesting a unique and organized transcriptional program across each phenotype.

There are several directions for this work that could help deepen our understanding and the implications of changes and loss in gene functional organization during aging. For example, as observed in our results, investigation on possible co-expression changes in crucial aging-related processes such as macroautophagy and stress response are appealing.

Future work will address the analysis of gene communities, as well as whole-genome-based over-representation analyses, such as GeneSet Enrichment Analysis (Subramanian et al., 2005), the use of deconvolution algorithms to analyze cell composition and proportion and their contribution to each phenotype, using single-cell data to analyze changes in trajectories throughout life, and finally, analyzing the co-expression networks of elderly individuals who have undergone interventions (pharmacological, dietary, or exercise) to identify those interventions that could prevent the loss of gene co-expression.